Time Varying R in Bicol Region as of October 12, 2020

The following figure shows the output plots: Epidemic Curve, Estimated R, and Explored Serial Interval Distribution

Computed R (Mean R) Value for Bicol Region on October 12 or Day 200

(Please ignore the warning message)

FALSE     Mean(R)     Std(R)
FALSE 1: 1.115605 0.09710092
FALSE    Quantile.0.025(R) Quantile.0.05(R) Quantile.0.25(R) Median(R)
FALSE 1:         0.9334172         0.960835         1.048667  1.112789
FALSE    Quantile.0.75(R) Quantile.0.95(R)
FALSE 1:         1.179473          1.27998

REFERENCES

packages used: dplyr, data.table, lubridate, reshape2, ggplot2, EpiEstim, epicontacts, googlesheets4, readxl

Help us improve our viz. Send a pull request at link

R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URLhttps://www.R-project.org/

Anne Cori (2020). EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves. R package version 2.2-3. https://CRAN.R-project.org/package=EpiEstim

Hadley Wickham and Jennifer Bryan (2019). readxl: Read Excel Files. R package version 1.3.1. https://CRAN.R-project.org/package=readxl

VP Nagraj, Thibaut Jombart, Nistara Randhawa, Bertrand Sudre, Finlay Campbell and Thomas Crellen (2017). epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts. R package version 1.1.0. https://CRAN.R-project.org/package=epicontacts

Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/

Jennifer Bryan (2020). googlesheets4: Access Google Sheets using the Sheets API V4. R package version 0.2.0. https://CRAN.R-project.org/package=googlesheets4

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016

Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.4.0. https://CRAN.R-project.org/package=stringr

Matt Dowle and Arun Srinivasan (2019). data.table: Extension of data.frame`. R package version 1.12.8. https://CRAN.R-project.org/package=data.table

JJ Allaire and Yihui Xie and Jonathan McPherson and JavierLuraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone (2020).rmarkdown: Dynamic Documents for R. R package version 2.1. URLhttps://rmarkdown.rstudio.com.

Hadley Wickham, Romain Fran?ois, Lionel Henry and Kirill M?ller (2020). dplyr: A Grammar of Data Manipulation. R package version 1.0.0.https://CRAN.R-project.org/package=dplyr

Anne Cori (2020). EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves. R package version 2.2-3. https://CRAN.R-project.org/package=EpiEstim

VP Nagraj, Thibaut Jombart, Nistara Randhawa, Bertrand Sudre, Finlay Campbell and Thomas Crellen (2017). epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts. R package version 1.1.0. https://CRAN.R-project.org/package=epicontacts

Garrett Grolemund, Hadley Wickham (2011). Dates and Times Made Easy with lubridate. Journal of Statistical Software, 40(3), 1-25. URL http://www.jstatsoft.org/v40/i03/

Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/

Yihui Xie (2020). knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.29.

Yihui Xie (2015) Dynamic Documents with R and knitr. 2nd edition. Chapman and Hall/CRC. ISBN 978-1498716963

Yihui Xie (2014) knitr: A Comprehensive Tool for Reproducible Research in R. In Victoria Stodden, Friedrich Leisch and Roger D. Peng, editors, Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595